the title seems to ask for a subjective opinion, which are generally frowned upon on SEs. It might be helpful to title your question with something more objective and something which can be answered with facts or information and not opinion.
– idiotprogrammerOct 14 '17 at 17:13

Remember that all epub files must be validly formatted. In other words, if you run it through this validator, it will give you zero errors. http://validator.idpf.org/

Then from epub, you can use Kindle Beta Previewer to convert to a kindle file.

An epub file is basically a zip file of various HTML files and package.opf. The package.opf will list the TOC so it's virtually a given that if you have a valid epub file, you will have a correctly formatted TOC menu.

If you are using content as a marketing device, I would be fine with keeping it in PDF form. Many people who read things have tablets which allow them to see PDF in its native format. EPUBs are better for content-heavy stuff and for viewing on multiple devices of different sizes.

I don't use the Adobe Indesign --> epub method, but if you are already comfortable with Adobe tools, this might be your best bet because they let you export to epub.

Obviously there's a lot more to say, but this information should give you enough to get started.

UPDATE: The question seems to ask specifically about how to create a beautiful ebook. That's hard to answer directly, but I can say that PDFs created via Adobe offer lots of options for font and pixel-perfect layout and illustrations that you're unlikely to find in an epub -- even on a robust reading system. You could argue that epub follows the responsive design paradigm, which means the end goal is to have a consistent reading experience on multiple platforms, whereas Adobe tools and workflow are more dedicated to one single form factor. I don't think I'm really being too controversial in saying that Adobe tools can produce lovely and complex designs and layouts, and it would take at least a decade before epub reading systems catch up. On the other hand, epub files are more functional and flexible and less dependent on having the right reading system to read it on. I have seen some amazing things produced for iBooks, but these are optimized only for one platform and not easily read on other platforms.

The question boils down to: do the benefits of designing for a single reading system outweigh the benefits of responsive design?